Preliminary results PLOS Biol
The design of the experiments (table with parameters) can be found here. But here is a brief description.
| PS | N_GENES_INITIAL | BITING_RATE_MEAN | N_LOCI | N_ALLELES_INITIAL |
|---|---|---|---|---|
| 01 | 120 | 0.1 | 2 | 12 |
| 02 | 1200 | 0.2 | 2 | 120 |
| 03 | 12000 | 0.5 | 2 | 1200 |
- PS: parameter space: 01,02,03 for low, medium, high diversity.
- exp: 000 is to run to checkpoint; 001 is the experiment itself (no seasonality)
I kept daily biting rates fixed to 1.
1. Basic variables for each scenario across regimes
1.1 diversity
In the complete neutrality, the number of circulating strains seems just too much. This is orders of magnitude more than the selection.
Selection
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 1"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 1"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 1"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 2"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 2"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 2"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 3"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 3"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 3"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 4"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 4"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 4"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 5"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 5"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 5"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 6"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 6"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 6"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 7"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 7"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 7"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 8"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 8"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 8"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 9"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 9"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 9"
## [1] "PS: 04 | Scenario: S | exp: 001 | run: 10"
## [1] "PS: 05 | Scenario: S | exp: 001 | run: 10"
## [1] "PS: 06 | Scenario: S | exp: 001 | run: 10"
Complete neutrality
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 1"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 1"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 1"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 2"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 2"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 2"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 3"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 3"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 3"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 4"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 4"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 4"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 5"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 5"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 5"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 6"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 6"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 6"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 7"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 7"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 7"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 8"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 8"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 8"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 9"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 9"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 9"
## [1] "PS: 04 | Scenario: N | exp: 001 | run: 10"
## [1] "PS: 05 | Scenario: N | exp: 001 | run: 10"
## [1] "PS: 06 | Scenario: N | exp: 001 | run: 10"
Generalized immunity
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 1"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 1"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 1"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 2"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 2"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 2"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 3"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 3"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 3"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 4"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 4"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 4"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 5"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 5"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 5"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 6"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 6"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 6"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 7"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 7"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 7"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 8"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 8"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 8"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 9"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 9"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 9"
## [1] "PS: 04 | Scenario: G | exp: 001 | run: 10"
## [1] "PS: 05 | Scenario: G | exp: 001 | run: 10"
## [1] "PS: 06 | Scenario: G | exp: 001 | run: 10"
1.2 EIR
The EIR for selection seems too low? For neutrality it is an order of magnitude more.
Selection
Complete neutrality
Generalized immunity
2. Compare scenarios for a given regime
Notice the order of magnitude difference in the number of repertoires
Low diversity & transmission
## [1] "Scenario: S | exp: 001 | run: 1"
## [1] "Scenario: N | exp: 001 | run: 1"
## [1] "Scenario: G | exp: 001 | run: 1"
## [1] "Scenario: S | exp: 001 | run: 2"
## [1] "Scenario: N | exp: 001 | run: 2"
## [1] "Scenario: G | exp: 001 | run: 2"
## [1] "Scenario: S | exp: 001 | run: 3"
## [1] "Scenario: N | exp: 001 | run: 3"
## [1] "Scenario: G | exp: 001 | run: 3"
## [1] "Scenario: S | exp: 001 | run: 4"
## [1] "Scenario: N | exp: 001 | run: 4"
## [1] "Scenario: G | exp: 001 | run: 4"
## [1] "Scenario: S | exp: 001 | run: 5"
## [1] "Scenario: N | exp: 001 | run: 5"
## [1] "Scenario: G | exp: 001 | run: 5"
## [1] "Scenario: S | exp: 001 | run: 6"
## [1] "Scenario: N | exp: 001 | run: 6"
## [1] "Scenario: G | exp: 001 | run: 6"
## [1] "Scenario: S | exp: 001 | run: 7"
## [1] "Scenario: N | exp: 001 | run: 7"
## [1] "Scenario: G | exp: 001 | run: 7"
## [1] "Scenario: S | exp: 001 | run: 8"
## [1] "Scenario: N | exp: 001 | run: 8"
## [1] "Scenario: G | exp: 001 | run: 8"
## [1] "Scenario: S | exp: 001 | run: 9"
## [1] "Scenario: N | exp: 001 | run: 9"
## [1] "Scenario: G | exp: 001 | run: 9"
## [1] "Scenario: S | exp: 001 | run: 10"
## [1] "Scenario: N | exp: 001 | run: 10"
## [1] "Scenario: G | exp: 001 | run: 10"
Medium diversity & transmission
## [1] "Scenario: S | exp: 001 | run: 1"
## [1] "Scenario: N | exp: 001 | run: 1"
## [1] "Scenario: G | exp: 001 | run: 1"
## [1] "Scenario: S | exp: 001 | run: 2"
## [1] "Scenario: N | exp: 001 | run: 2"
## [1] "Scenario: G | exp: 001 | run: 2"
## [1] "Scenario: S | exp: 001 | run: 3"
## [1] "Scenario: N | exp: 001 | run: 3"
## [1] "Scenario: G | exp: 001 | run: 3"
## [1] "Scenario: S | exp: 001 | run: 4"
## [1] "Scenario: N | exp: 001 | run: 4"
## [1] "Scenario: G | exp: 001 | run: 4"
## [1] "Scenario: S | exp: 001 | run: 5"
## [1] "Scenario: N | exp: 001 | run: 5"
## [1] "Scenario: G | exp: 001 | run: 5"
## [1] "Scenario: S | exp: 001 | run: 6"
## [1] "Scenario: N | exp: 001 | run: 6"
## [1] "Scenario: G | exp: 001 | run: 6"
## [1] "Scenario: S | exp: 001 | run: 7"
## [1] "Scenario: N | exp: 001 | run: 7"
## [1] "Scenario: G | exp: 001 | run: 7"
## [1] "Scenario: S | exp: 001 | run: 8"
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## [1] "Scenario: S | exp: 001 | run: 9"
## [1] "Scenario: N | exp: 001 | run: 9"
## [1] "Scenario: G | exp: 001 | run: 9"
## [1] "Scenario: S | exp: 001 | run: 10"
## [1] "Scenario: N | exp: 001 | run: 10"
## [1] "Scenario: G | exp: 001 | run: 10"
High diversity & transmission
## [1] "Scenario: S | exp: 001 | run: 1"
## [1] "Scenario: N | exp: 001 | run: 1"
## [1] "Scenario: G | exp: 001 | run: 1"
## [1] "Scenario: S | exp: 001 | run: 2"
## [1] "Scenario: N | exp: 001 | run: 2"
## [1] "Scenario: G | exp: 001 | run: 2"
## [1] "Scenario: S | exp: 001 | run: 3"
## [1] "Scenario: N | exp: 001 | run: 3"
## [1] "Scenario: G | exp: 001 | run: 3"
## [1] "Scenario: S | exp: 001 | run: 4"
## [1] "Scenario: N | exp: 001 | run: 4"
## [1] "Scenario: G | exp: 001 | run: 4"
## [1] "Scenario: S | exp: 001 | run: 5"
## [1] "Scenario: N | exp: 001 | run: 5"
## [1] "Scenario: G | exp: 001 | run: 5"
## [1] "Scenario: S | exp: 001 | run: 6"
## [1] "Scenario: N | exp: 001 | run: 6"
## [1] "Scenario: G | exp: 001 | run: 6"
## [1] "Scenario: S | exp: 001 | run: 7"
## [1] "Scenario: N | exp: 001 | run: 7"
## [1] "Scenario: G | exp: 001 | run: 7"
## [1] "Scenario: S | exp: 001 | run: 8"
## [1] "Scenario: N | exp: 001 | run: 8"
## [1] "Scenario: G | exp: 001 | run: 8"
## [1] "Scenario: S | exp: 001 | run: 9"
## [1] "Scenario: N | exp: 001 | run: 9"
## [1] "Scenario: G | exp: 001 | run: 9"
## [1] "Scenario: S | exp: 001 | run: 10"
## [1] "Scenario: N | exp: 001 | run: 10"
## [1] "Scenario: G | exp: 001 | run: 10"
3. Edge weight values
Selection
Complete Neutrality
Generalized immunity
4. Cutoff (SELECTION)
Cutoff is based on the selection case, so we will look at it more closely. Then we will compare the behavior of the system across scenarios at different cutoffs.
Examples for modules
Persistence and relative persistence
Persistence (months) 
Relative persistence 
Modules per layer
Repertoires in a module
5. Cutoff – scenario comparison
Examples for modules
Persistence and relative persistence
Module persistence
Persistence (months) 
Relative persistence 
Repertoire persistence
Persistence (months) 
Relative persistence 
Modules per layer
Repertoires in a module
“Temporal diversity”
All scenarios: 
Compare this to the diversity (wihtout the temporal dimension): 
Selection
Neutral
Generalized
